<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8">
<META NAME="GENERATOR" CONTENT="GtkHTML/4.6.6">
</HEAD>
<BODY>
Barry,<BR>
<BR>
thank you for the clarification!<BR>
<BR>
Best,<BR>
Michele<BR>
<BR>
<BR>
On Wed, 2015-07-01 at 20:02 -0500, Barry Smith wrote:
<BLOCKQUOTE TYPE=CITE>
<PRE>
Ahh yes, I see. I have added the following text to PetscOptionsInsertFile() to clarify
Usually, instead of using this command, one should list the file name in the call to PetscInitialize(), this insures that certain options
such as -log_summary or -malloc_debug are processed properly. This routine only sets options into the options database that will be processed by later
calls to XXXSetFromOptions() it should not be used for options listed under PetscInitialize().
<FONT COLOR="#737373">> On Jul 1, 2015, at 4:52 PM, Michele Rosso <<A HREF="mailto:mrosso@uci.edu">mrosso@uci.edu</A>> wrote:</FONT>
<FONT COLOR="#737373">> </FONT>
<FONT COLOR="#737373">> Hi Barry,</FONT>
<FONT COLOR="#737373">> </FONT>
<FONT COLOR="#737373">> I accidentally found out what triggers the problem with log_summary.</FONT>
<FONT COLOR="#737373">> If I specify log_summary from command line, it works as expected. If instead I open and load an options file with -log_summary in it,</FONT>
<FONT COLOR="#737373">> the output is incomplete.</FONT>
<FONT COLOR="#737373">> I am actually concerned about using options files now because this weird behavior could affect the correct loading of other options as well.</FONT>
<FONT COLOR="#737373">> </FONT>
<FONT COLOR="#737373">> Michele </FONT>
<FONT COLOR="#737373">> </FONT>
<FONT COLOR="#737373">> </FONT>
<FONT COLOR="#737373">> On Fri, 2015-06-05 at 21:34 -0500, Barry Smith wrote:</FONT>
<FONT COLOR="#737373">>> [NID 04001] 2015-06-04 19:07:24 Apid 25022256: initiated application termination</FONT>
<FONT COLOR="#737373">>> Application 25022256 exit signals: Killed</FONT>
<FONT COLOR="#737373">>> Application 25022256 resources: utime ~271s, stime ~15107s, Rss ~188536, inblocks ~5078831, outblocks ~12517984</FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> Usually this kind of message indicates that either the OS or the batch system killed the process for some reason: often because it ran out of time or maybe memory.</FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> Can you run in batch with a request for more time? Do smaller jobs run through ok?</FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> If utime means user time and stime means system time then this is very bad, the system time is HUGE relative to the user time.</FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> Barry</FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> > On Jun 5, 2015, at 9:22 PM, Michele Rosso <<A HREF="mailto:mrosso@uci.edu">mrosso@uci.edu</A>> wrote:</FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > Hi,</FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > I am checking the performances of my code via -log_summary, but the output is incomplete (please see attached) file.</FONT>
<FONT COLOR="#737373">>> > I configured petsc with the following options:</FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > if __name__ == '__main__':</FONT>
<FONT COLOR="#737373">>> > import sys</FONT>
<FONT COLOR="#737373">>> > import os</FONT>
<FONT COLOR="#737373">>> > sys.path.insert(0, os.path.abspath('config'))</FONT>
<FONT COLOR="#737373">>> > import configure</FONT>
<FONT COLOR="#737373">>> > configure_options = [</FONT>
<FONT COLOR="#737373">>> > '--with-batch=1 ',</FONT>
<FONT COLOR="#737373">>> > '--known-mpi-shared=0 ',</FONT>
<FONT COLOR="#737373">>> > '--known-mpi-shared-libraries=0',</FONT>
<FONT COLOR="#737373">>> > '--known-memcmp-ok ',</FONT>
<FONT COLOR="#737373">>> > '--with-blas-lapack-lib=-L/opt/acml/5.3.1/gfortran64/lib -lacml',</FONT>
<FONT COLOR="#737373">>> > '--COPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ',</FONT>
<FONT COLOR="#737373">>> > '--FOPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ',</FONT>
<FONT COLOR="#737373">>> > '--CXXOPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ',</FONT>
<FONT COLOR="#737373">>> > '--with-x=0 ',</FONT>
<FONT COLOR="#737373">>> > '--with-debugging=0',</FONT>
<FONT COLOR="#737373">>> > '--with-clib-autodetect=0 ',</FONT>
<FONT COLOR="#737373">>> > '--with-cxxlib-autodetect=0 ',</FONT>
<FONT COLOR="#737373">>> > '--with-fortranlib-autodetect=0 ',</FONT>
<FONT COLOR="#737373">>> > '--with-shared-libraries=0 ',</FONT>
<FONT COLOR="#737373">>> > '--with-mpi-compilers=1 ',</FONT>
<FONT COLOR="#737373">>> > '--with-cc=cc ',</FONT>
<FONT COLOR="#737373">>> > '--with-cxx=CC ',</FONT>
<FONT COLOR="#737373">>> > '--with-fc=ftn ',</FONT>
<FONT COLOR="#737373">>> > # '--with-64-bit-indices',</FONT>
<FONT COLOR="#737373">>> > '--download-hypre=1',</FONT>
<FONT COLOR="#737373">>> > '--download-blacs=1 ',</FONT>
<FONT COLOR="#737373">>> > '--download-scalapack=1 ',</FONT>
<FONT COLOR="#737373">>> > '--download-superlu_dist=1 ',</FONT>
<FONT COLOR="#737373">>> > '--download-metis=1 ',</FONT>
<FONT COLOR="#737373">>> > '--download-parmetis=1 ',</FONT>
<FONT COLOR="#737373">>> > ]</FONT>
<FONT COLOR="#737373">>> > configure.petsc_configure(configure_options)</FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > Any idea about this issue?</FONT>
<FONT COLOR="#737373">>> > Thanks,</FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > Michele</FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > </FONT>
<FONT COLOR="#737373">>> > <log_summary></FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">>> </FONT>
<FONT COLOR="#737373">> </FONT>
</PRE>
</BLOCKQUOTE>
<BR>
</BODY>
</HTML>